various doc updates

README.md

@@ -15,32 +15,65 @@ to output to multiple formats.
 Requirements:
 * python >= 3.11
 * numpy
-* klamath (optional, used for `gdsii` i/o)
+* klamath (used for GDSII i/o)
-* matplotlib (optional, used for `visualization` functions and `text`)
+
-* ezdxf (optional, used for `dxf` i/o)
+Optional requirements:
-* fatamorgana (optional, used for `oasis` i/o)
+* `ezdxf` (DXF i/o): ezdxf
-* svgwrite (optional, used for `svg` output)
+* `oasis` (OASIS i/o): fatamorgana
-* freetype (optional, used for `text`)
+* `svg` (SVG output): svgwrite
+* `visualization` (shape plotting): matplotlib
+* `text` (`Text` shape): matplotlib, freetype
 
 
 Install with pip:
 ```bash
-pip install 'masque[visualization,oasis,dxf,svg,text]'
+pip install 'masque[oasis,dxf,svg,visualization,text]'
 ```
 
-Alternatively, install from git
+## Overview
-```bash
+
-pip install git+https://mpxd.net/code/jan/masque.git@release
+A layout consists of a hierarchy of `Pattern`s stored in a single `Library`.
-```
+Each `Pattern` can contain `Ref`s pointing at other patterns, `Shape`s, and `Label`s.
+
+`masque` departs from several "classic" GDSII paradigms:
+- Layer info for `Shape`ss and `Label`s is not stored in the individual shape and label objects.
+    Instead, the layer is determined by the key for the container dict (e.g. `pattern.shapes[layer]`).
+    * This simplifies many common tasks: filtering `Shape`s by layer, remapping layers, and checking if
+        a layer is empty.
+    * Technically, this allows reusing the same shape or label object across multiple layers. This isn't
+        part of the standard workflow since a mixture of single-use and multi-use shapes could be confusing.
+    * This is similar to the approach used in [KLayout](https://www.klayout.de)
+- `Ref` target names are also determined in the key of the container dict (e.g. `pattern.refs[target_name]`).
+    * This similarly simplifies filtering `Ref`s by target name, updating to a new target, and checking
+        if a given `Pattern` is referenced.
+- `Pattern` names are set by their containing `Library` and are not stored in the `Pattern` objects.
+    * This guarantees that there are no duplicate pattern names within any given `Library`.
+    * Likewise, enumerating all the names (and all the `Pattern`s) in a `Library` is straightforward.
+- Each `Ref`, `Shape`, or `Label` can be repeated multiple times by attaching a `repetition` object to it.
+    * This is similar to how OASIS reptitions are handled, and provides extra flexibility over the GDSII
+        approach of only allowing arrays through AREF (`Ref` + `repetition`).
+- `Label`s do not have an orientation or presentation
+    * This is in line with how they are used in practice, and how they are represented in OASIS.
+- Non-polygonal `Shape`s are allowed. For example, elliptical arcs are a basic shape type.
+    * This enables compatibility with OASIS (e.g. circles) and other formats.
+    * `Shape`s provide a `.to_polygons()` method for GDSII compatibility.
+- Most coordinate values are stored as 64-bit floats internally.
+    * 1 earth radii in nanometers (6e15) is still represented without approximation (53 bit mantissa -> 2^53 > 9e15)
+    * Operations that would otherwise clip/round on are still represented approximately.
+    * Memory usage is usually dominated by other Python overhead.
+
 
 ## Glossary
-- `Library`: OASIS or GDS "library" or file (a collection of named cells)
+- `Library`: A collection of named cells. OASIS or GDS "library" or file.
-- `Pattern`: OASIS or GDS "Cell", DXF "Block"
+- `Pattern`: A collection of geometry, text labels, and reference to other patterns.
-- `Ref`: GDS "AREF/SREF", OASIS "Placement"
+        OASIS or GDS "Cell", DXF "Block".
-- `Shape`: OASIS or GDS "Geometry element", DXF "LWPolyline" or "Polyline"
+- `Ref`: A reference to another pattern. GDS "AREF/SREF", OASIS "Placement".
-- `repetition`: OASIS "repetition". GDS "AREF" is a `Ref` combined with a `Grid` repetition.
+- `Shape`: Individual geometric entity. OASIS or GDS "Geometry element", DXF "LWPolyline" or "Polyline".
-- `Label`: OASIS, GDS, DXF "Text".
+- `repetition`: Repetition operation. OASIS "repetition".
-- `annotation`: OASIS or GDS "property"
+        GDS "AREF" is a `Ref` combined with a `Grid` repetition.
+- `Label`: Text label. Not rendered into geometry. OASIS, GDS, DXF "Text".
+- `annotation`: Additional metadata. OASIS or GDS "property".
+
 
 
 ## TODO
@@ -48,7 +81,6 @@ pip install git+https://mpxd.net/code/jan/masque.git@release
 * Better interface for polygon operations (e.g. with `pyclipper`)
     - de-embedding
     - boolean ops
-* DOCS DOCS DOCS
 * Tests tests tests
 * check renderpather
 * pather and renderpather examples

masque/file/gdsii.py

@@ -495,12 +495,12 @@ def _labels_to_texts(labels: dict[layer_t, list[Label]]) -> list[klamath.element
                 xy=xy,
                 string=label.string.encode('ASCII'),
                 properties=properties,
-                presentation=0,  # TODO maybe set some of these?
+                presentation=0,  # font number & alignment -- unused by us
-                angle_deg=0,
+                angle_deg=0,     # rotation -- unused by us
-                invert_y=False,
+                invert_y=False,  # inversion -- unused by us
-                width=0,
+                width=0,         # stroke width -- unused by us
-                path_type=0,
+                path_type=0,     # text path endcaps, unused
-                mag=1,
+                mag=1,           # size -- unused by us
                 )
             texts.append(text)
     return texts

masque/library.py

@@ -2,7 +2,7 @@
 Library classes for managing unique name->pattern mappings and
  deferred loading or creation.
 
-# TODO documentn all library classes
+# TODO documennt all library classes
 # TODO toplevel documentation of library, classes, and abstracts
 """
 from typing import Callable, Self, Type, TYPE_CHECKING, cast

masque/pattern.py

@@ -1,5 +1,6 @@
 """
- Base object representing a lithography mask.
+  Object representing a one multi-layer lithographic layout.
+  A single level of hierarchical references is included.
 """
 from typing import Callable, Sequence, cast, Mapping, Self, Any, Iterable, TypeVar, MutableMapping
 import copy
@@ -27,7 +28,7 @@ logger = logging.getLogger(__name__)
 class Pattern(PortList, AnnotatableImpl, Mirrorable):
     """
     2D layout consisting of some set of shapes, labels, and references to other Pattern objects
-     (via Ref). Shapes are assumed to inherit from masque.shapes.Shape or provide equivalent functions.
+     (via Ref). Shapes are assumed to inherit from `masque.shapes.Shape` or provide equivalent functions.
     """
     __slots__ = (
         'shapes', 'labels', 'refs', '_ports',
@@ -864,6 +865,19 @@ TT = TypeVar('TT')
 
 
 def chain_elements(*args: Mapping[Any, Iterable[TT]]) -> Iterable[TT]:
+    """
+    Iterate over each element in one or more {layer: elements} mappings.
+
+    Useful when you want to do some operation on all shapes and/or labels,
+    disregarding which layer they are on.
+
+    Args:
+        *args: One or more {layer: [element0, ...]} mappings.
+            Can also be applied to e.g. {target: [ref0, ...]} mappings.
+
+    Returns:
+        An iterable containing all elements, regardless of layer.
+    """
     return chain(*(chain.from_iterable(aa.values()) for aa in args))
 
 
@@ -871,6 +885,20 @@ def map_layers(
         elements: Mapping[layer_t, Sequence[TT]],
         map_layer: Callable[[layer_t], layer_t],
         ) -> defaultdict[layer_t, list[TT]]:
+    """
+    Move all the elements from one layer onto a different layer.
+    Can also handle multiple such mappings simultaneously.
+
+    Args:
+        elements: Mapping of {old_layer: geometry_or_labels}.
+        map_layer: Callable which may be called with each layer present in `elements`,
+            and should return the new layer to which it will be mapped.
+            A simple example which maps `old_layer` to `new_layer` and leaves all others
+            as-is would look like `lambda layer: {old_layer: new_layer}.get(layer, layer)`
+
+    Returns:
+        Mapping of {new_layer: geometry_or_labels}
+    """
     new_elements: defaultdict[layer_t, list[TT]] = defaultdict(list)
     for old_layer, seq in elements.items():
         new_layer = map_layer(old_layer)
@@ -882,6 +910,20 @@ def map_targets(
         refs: Mapping[str | None, Sequence[Ref]],
         map_target: Callable[[str | None], str | None],
         ) -> defaultdict[str | None, list[Ref]]:
+    """
+    Change the target of all references to a given cell.
+    Can also handle multiple such mappings simultaneously.
+
+    Args:
+        refs: Mapping of {old_target: ref_objects}.
+        map_target: Callable which may be called with each target present in `refs`,
+            and should return the new target to which it will be mapped.
+            A simple example which maps `old_target` to `new_target` and leaves all others
+            as-is would look like `lambda target: {old_target: new_target}.get(target, target)`
+
+    Returns:
+        Mapping of {new_target: ref_objects}
+    """
     new_refs: defaultdict[str | None, list[Ref]] = defaultdict(list)
     for old_target, seq in refs.items():
         new_target = map_target(old_target)

masque/ref.py

@@ -1,9 +1,7 @@
 """
- Ref provides basic support for nesting Pattern objects within each other, by adding
+ Ref provides basic support for nesting Pattern objects within each other.
-  offset, rotation, scaling, and other such properties to the reference.
+ It carries offset, rotation, mirroring, and scaling data for each individual instance.
 """
-#TODO more top-level documentation for ref
-
 from typing import Mapping, TYPE_CHECKING, Self
 import copy
 
@@ -28,10 +26,15 @@ class Ref(
         PivotableImpl, Copyable, RepeatableImpl, AnnotatableImpl,
         ):
     """
-    `Ref` provides basic support for nesting Pattern objects within each other, by adding
+    `Ref` provides basic support for nesting Pattern objects within each other.
-     offset, rotation, scaling, and associated methods.
 
-    Note: Order is (mirror, rotate, scale, translate, repeat)
+    It containts the transformation (mirror, rotation, scale, offset, repetition)
+    and annotations for a single instantiation of a `Pattern`.
+
+    Note that the target (i.e. which pattern a `Ref` instantiates) is not stored within the
+    `Ref` itself, but is specified by the containing `Pattern`.
+
+    Order of operations is (mirror, rotate, scale, translate, repeat).
     """
     __slots__ = (
         '_mirrored',

masque/shapes/path.py

@@ -26,6 +26,9 @@ class Path(Shape):
     A path, consisting of a bunch of vertices (Nx2 ndarray), a width, an end-cap shape,
         and an offset.
 
+    Note that the setter for `Path.vertices` may (but may not) create a copy of the
+      passed vertex coordinates. See `numpy.array(..., copy=False)` for details.
+
     A normalized_form(...) is available, but can be quite slow with lots of vertices.
     """
     __slots__ = (
@@ -61,12 +64,14 @@ class Path(Shape):
     def cap(self) -> PathCap:
         """
         Path end-cap
+
+        Note that `cap_extensions` will be reset to default values if
+         `cap` is changed away from `PathCap.SquareCustom`.
         """
         return self._cap
 
     @cap.setter
     def cap(self, val: PathCap) -> None:
-        # TODO: Document that setting cap can change cap_extensions
         self._cap = PathCap(val)
         if self.cap != PathCap.SquareCustom:
             self.cap_extensions = None
@@ -80,6 +85,9 @@ class Path(Shape):
         """
         Path end-cap extension
 
+        Note that `cap_extensions` will be reset to default values if
+         `cap` is changed away from `PathCap.SquareCustom`.
+
         Returns:
             2-element ndarray or `None`
         """
@@ -101,13 +109,16 @@ class Path(Shape):
     @property
     def vertices(self) -> Any:  # mypy#3004  NDArray[numpy.float64]]:
         """
-        Vertices of the path (Nx2 ndarray: `[[x0, y0], [x1, y1], ...]`)
+        Vertices of the path (Nx2 ndarray: `[[x0, y0], [x1, y1], ...]`
+
+        When setting, note that a copy of the provided vertices may or may not be made,
+        following the rules from `numpy.array(.., copy=False)`.
         """
         return self._vertices
 
     @vertices.setter
     def vertices(self, val: ArrayLike) -> None:
-        val = numpy.array(val, dtype=float)                 # TODO document that these might not be copied
+        val = numpy.array(val, dtype=float)
         if len(val.shape) < 2 or val.shape[1] != 2:
             raise PatternError('Vertices must be an Nx2 array')
         if val.shape[0] < 2:
@@ -218,7 +229,7 @@ class Path(Shape):
         Returns:
             The resulting Path object
         """
-        # TODO: needs testing
+        # TODO: Path.travel() needs testing
         direction = numpy.array([1, 0])
 
         verts = [numpy.zeros(2)]

masque/shapes/polygon.py

@@ -18,7 +18,7 @@ class Polygon(Shape):
        implicitly-closed boundary, and an offset.
 
     Note that the setter for `Polygon.vertices` may (but may not) create a copy of the
-      passed vertex coordinates. See `numpy.array()` for details.
+      passed vertex coordinates. See `numpy.array(..., copy=False)` for details.
 
     A `normalized_form(...)` is available, but can be quite slow with lots of vertices.
     """
@@ -36,12 +36,15 @@ class Polygon(Shape):
     def vertices(self) -> Any:        # mypy#3004   NDArray[numpy.float64]:
         """
         Vertices of the polygon (Nx2 ndarray: `[[x0, y0], [x1, y1], ...]`)
+
+        When setting, note that a copy of the provided vertices may or may not be made,
+        following the rules from `numpy.array(.., copy=False)`.
         """
         return self._vertices
 
     @vertices.setter
     def vertices(self, val: ArrayLike) -> None:
-        val = numpy.array(val, dtype=float)             # note that this hopefully won't create a copy
+        val = numpy.array(val, dtype=float)
         if len(val.shape) < 2 or val.shape[1] != 2:
             raise PatternError('Vertices must be an Nx2 array')
         if val.shape[0] < 3: